I've just uploaded my first model and the thumbnail shows it on it's side. I feel the model has an obvious base so how can I be sure it will use this base when the part is made? Is the thumbnail any indication of the orientation used when printed?

Model orientation in the thumbnail has no connection to print orientation - for the former, ensure Z axis is pointing up
in whatever software you use, or use the free version of netfabb studio basic to reorient your model before uploading.
Print orientation is currently decided by the shapeways crew based on a combination of past experience and printer
utilization (models are not printed individually, but in carefully stacked batches - also the layered printing process may
produce visible stair-stepping on some face of the model, so the model may be reoriented so that its "obvious" base
is taking the brunt of that).